cellmaps-utils

============================= Cell Maps Pipeline Utilities

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Contains utilities needed by various tools in the cell maps toolkit.

• Free software: MIT license
• Documentation: https://cellmaps-utils.readthedocs.io.
• Source code: https://github.com/idekerlab/cellmaps_utils

Dependencies

• fairscape-cli <https://pypi.org/project/fairscape-cli>__
• scipy <https://pypi.org/project/scipy>__
• scikit-learn <https://pypi.org/project/scikit-learn>__
• pandas <https://pypi.org/project/pandas>__
• numpy <https://pypi.org/project/numpy>__
• dill <https://pypi.org/project/dill>__

Compatibility

• Python 3.8+

Installation

.. code-block::

git clone https://github.com/idekerlab/cellmaps_utils cd cellmaps_utils make dist pip install dist/cellmaps_utils*whl

Run make command with no arguments to see other build/deploy options including creation of Docker image

.. code-block::

make

Output:

.. code-block::

clean remove all build, test, coverage and Python artifacts clean-build remove build artifacts clean-pyc remove Python file artifacts clean-test remove test and coverage artifacts lint check style with flake8 test run tests quickly with the default Python test-all run tests on every Python version with tox coverage check code coverage quickly with the default Python docs generate Sphinx HTML documentation, including API docs servedocs compile the docs watching for changes testrelease package and upload a TEST release release package and upload a release dist builds source and wheel package install install the package to the active Python's site-packages

Before running tests, please install pip install -r requirements_dev

For developers

To deploy development versions of this package

Below are steps to make changes to this code base, deploy, and then run
against those changes.

#. Make changes

Modify code in this repo as desired

#. Build and deploy

.. code-block::

    # From base directory of this repo cellmaps_hierarchyeval
    pip uninstall cellmaps_utils -y ; make clean dist; pip install dist/cellmaps_utils*whl



Credits
-------

This package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template


.. _Cookiecutter: https://github.com/audreyr/cookiecutter
.. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage
.. _NDEx: http://www.ndexbio.org



=======
History
=======

0.5.0 (2024-09-05)
------------------

* Add ``HiDeFToHierarchyConverter``, a class to convert a edge list and node list
  in HiDeF format to hierarchy in HCX.
* Add ``InteractomeToDDOTConverter`` and ``DDOTToInteractomeConverter``, classes to convert network in
  CX2 format to DDOT format and vice versa, ``HierarchyToDDOTConverter`` and ``DDOTToHierarchyConverter``,
  classes to convert hierarchy network in HCX format to DDOT and vice versa.

0.4.0 (2024-07-02)
-------------------

* Updated provenance utils, added checks in for missing data in input RO-Crate,
  and allowing to continue but logging errors in the process

* Add ``HierarchyToHiDeFConverter``, a class to convert a hierarchy network
  (in CX2 format) to a HiDeF format nodes and edges lists.

* Add ``NDExHierarchyUploader``, a class for uploading hierarchy and
  its parent network to NDEx.

* Updated ``cellmaps_utilscmd.py`` ``apmsconverter``, ``ifconverter``,
  ``crisprconverter`` to support tissue as well as output
  ``data_info.json`` file to resulting RO-Crate so subsequent tools can
  more easily get provenance information


* Updated ``cellmaps_utilscmd.py crisprconverter`` to consume ``.h5ad``
  files and updated readme.txt file

0.3.0 (2024-04-15)
-------------------

* Bumped fairscape-cli dependency to ``0.2.0``


0.2.0 (2024-02-20)
------------------

* Bumped fairscape-cli dependency to ``0.1.14`` to support schemas

* Added support for ``schema`` to **data_dict** parameter in ``ProvenanceUtil.register_dataset()``

* Added ``--release`` flag to ``cellmaps_utilscmd.py rocratetable`` and
  in output table renamed "Name of Computation" to "Name" as well as
  added "Type", "Cell Line", "Treatment", "Gene set", and "Version" to
  table output

* Set default logging level to ``ERROR`` for ``cellmaps_utilscmd.py`` command

0.1.0 (2024-01-01)
------------------

* First release on PyPI.